SMTL ID : 6spw.1

Structure of protein kinase CK2 catalytic subunit with the CK2beta-competitive bisubstrate inhibitor ARC3140

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

3 x DAS- ASP- ASP- ASP- ASP- ASP- LYS: ARC3140(Non-covalent)

DAS-ASP-ASP-ASP-ASP-ASP-LYS.1: 20 residues within 4Å: Chain A: Y.50, K.77, R.80, R.155, D.156, K.158, G.177, L.178, E.180, E.187, Y.188, N.189, R.191, V.192, A.193, S.194, R.195, K.198, Q.207 Ligands: A0Z.5 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:Y.50, A:E.180 Hydrogen bonds: A:R.80, A:R.80, A:R.155, A:K.158, A:K.158, A:E.180, A:E.180, A:N.189, A:N.189, A:R.191, A:R.195, A:Q.207 Water bridges: A:N.161, A:Q.186, A:R.195 Salt bridges: A:K.76, A:R.80, A:R.155, A:K.158, A:R.191, A:R.195, A:K.198 DAS-ASP-ASP-ASP-ASP-ASP-LYS.2: 2 residues within 4Å: Chain A: R.47 Ligands: A0Z.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.47 DAS-ASP-ASP-ASP-ASP-ASP-LYS.3: 5 residues within 4Å: Chain A: G.3, D.266, P.267, R.268 Ligands: A0Z.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.266, A:R.268 Water bridges: A:G.3, A:G.3

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 1 residues within 4Å: Chain A: T.326 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.326

3 x A0Z: 8-[4,5,6,7-tetrakis(iodanyl)benzimidazol-1-yl]octanoic acid(Non-covalent)

A0Z.5: 14 residues within 4Å: Chain A: R.47, G.48, K.49, V.53, V.66, I.95, F.113, E.114, V.116, K.158, M.163, I.174, D.175 Ligands: DAS-ASP-ASP-ASP-ASP-ASP-LYS.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.158 Water bridges: A:D.175 Halogen bonds: A:V.116 A0Z.6: 10 residues within 4Å: Chain A: Q.36, Y.39, L.41, K.44, E.52, I.69, V.101, T.108, A.110 Ligands: DAS-ASP-ASP-ASP-ASP-ASP-LYS.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.41, A:E.52, A:I.69 Hydrogen bonds: A:K.44 Halogen bonds: A:Y.39, A:T.108 A0Z.7: 8 residues within 4Å: Chain A: D.237, Y.239, D.240, D.266, R.268, F.269, I.272 Ligands: DAS-ASP-ASP-ASP-ASP-ASP-LYS.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.239, A:Y.239 Hydrogen bonds: A:R.268 Water bridges: A:R.268 Halogen bonds: A:D.237, A:D.240

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pietsch, M. et al., Unexpected CK2 beta-antagonistic functionality of bisubstrate inhibitors targeting protein kinase CK2. Bioorg.Chem. (2020)

Release Date

2020-01-29

Peptides

Casein kinase II subunit alpha: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Casein kinase II subunit alpha

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